Personally I'd try and avoid doing this altogether.
You're masking the problem rather than solving it.
If an index is worth adding to a single customer's database for example, it's probably worth adding to all customer databases. Otherwise the same issues will occur repeatedly going forward.
I understand the need for rapid support, but having databases which are fundamentally different on different workstations is only going to cause more problems moving forward, for example in recreating bugs.
It also adds a potential user "fiddle factor" once they learn how to do this and if the application is left on their machine (i.e. "I wonder what happens if I change this value?").
Either modify the current application (legacy or not) to add the appropriate indexes on startup, or create a seperate small "hotfix" program that adds the indexes and require your customers to run it.
The suggestion above that these are written using VBScript is perfectly reasonable. The key is that the databas echanges are repeatable and that you can track what changes have been made where.
If data itself needs modification, then why was this data written badly in the first place? Maybe the application can be appropriately modified so that this can be prevented in the first place? This would avoid the same issue happening with other databases.